Related papers: Cis-Regulatory Modules Drive Dynamic Patterns of a…
Synchronization has been reported for a wide range of self-oscillating systems. However, even though it has been predicted theoretically for several decades, the experimental realization of phase self-oscillation, sometimes called phase…
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian…
Many cells use calcium signalling to carry information from the extracellular side of the plasma membrane to targets in their interior. Since virtually all cells employ a network of biochemical reactions for Ca2+ signalling, much effort has…
We study the dynamical properties of small regulatory networks treated as non autonomous dynamical systems called modules when working inside larger networks or, equivalently when subject to external signal inputs. Particular emphasis is…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
In the design of cellular manufacturing systems (CMS), numerous technological and managerial decisions must be made at both the design and operational stages. The first step in designing a CMS involves grouping parts and machines. In this…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the…
Neuronal and glial cells release diverse proteoglycans and glycoproteins, which aggregate in the extracellular space and form the extracellular matrix (ECM) that may in turn regulate major cellular functions. Brain cells also release…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Computational approaches which emulate in-vivo nervous system are needed to investigate mechanisms of the brain to orchestrate behavior. Such approaches must integrate a series of biophysical models encompassing the nervous system, muscles,…
Modulation recognition is a challenging task while performing spectrum sensing in a cognitive radio setup. Recently, the use of deep convolutional neural networks (CNNs) has shown to achieve state-of-the-art accuracy for modulation…
Similar activity patterns may arise from model neural networks with distinct coupling properties and individual unit dynamics. These similar patterns may, however, respond differently to parameter variations and, specifically, to tuning of…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
In this paper we use a continuous model to describe the development of a single cell lineage following the committal of stem cells. Three separate controls are implemented in the model, namely the proliferative control of stem cells, the…
Traditional artificial neural networks consist of nodes with non-oscillatory dynamics. Biological neural networks, on the other hand, consist of oscillatory components embedded in an oscillatory environment. Motivated by this feature of…
Human pluripotent stem cells (hPSCs) have promising clinical applications in regenerative medicine, drug-discovery and personalised medicine due to their potential to differentiate into all cell types, a property know as pluripotency. A…
Model order reduction techniques simplify high-dimensional dynamical systems by deriving lower-dimensional models that retain essential system characteristics. These techniques are crucial for the controller design of complex systems while…